# HG changeset patch
# User trinity_ctat
# Date 1506965347 14400
# Node ID b5d906ce0f06f696b7d08b1fd5fb40f4ab0f3605
# Parent  6f54e220d0353e5555f99dec5a647a3e5a370974
Adding some debugging statements.

diff -r 6f54e220d035 -r b5d906ce0f06 analyze_diff_exp_wrapper.py
--- a/analyze_diff_exp_wrapper.py	Mon Oct 02 12:55:27 2017 -0400
+++ b/analyze_diff_exp_wrapper.py	Mon Oct 02 13:29:07 2017 -0400
@@ -56,15 +56,26 @@
 Cvalue=sys.argv[4]
 
 def run_command(cmd):
-    print "The command used: " + cmd
-    pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
-    pipe.wait()
-    ret= pipe.returncode
+    # 2017-10-02
+    # Cicada Dennis put the subprocess command in a try/except statement.
+    # Errors were going undetected the way it was written previously.
+    try:
+        pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+        cmd_stdout, cmd_stderr = pipe.communicate()
+    except:
+        msg = "ERROR while running command:\n\t" + cmd
+        sys.stderr.write(msg)
+        raise
+    
+    sys.stdout.write(cmd_stdout)
+    ret = pipe.returncode
     if ret:
         print "command died: " + str(ret)
-        print pipe.stderr.readlines()
+        sys.stderr.write(cmd_stderr)
         sys.exit(ret)
     else:
+        # Any error output written to stdout instead of stderr, since no error has occurred.
+        sys.stderr.write(cmd_stderr) 
         return
 
 print ""